Wednesday, May 27, 2009

ART/SCIENCE FUSION STUDENTS EXHIBIT PHOTOGRAPHY AND A CERAMIC MOSAIC MURAL, THE FACE OF DARWIN

The final student exhibition for "Photography: Bridging Art and Science," a Science and Society Program class taught by Terry Nathan as a part of the Art/Science Fusion series at the University of California, Davis (UC Davis), will be held at the Buehler Alumni and Visitors Center on the University of California, Davis campus beginning June 3 and continuing through July 3. The exhibit features over 50 student photographs exploring the conceptual connections between art and science and the role of art and science on the UC Davis campus. The opening reception, which is free and open to the public, is June 4 from 3-5 p.m.

Also included in the exhibition is a ceramic mosaic mural, The Face of Darwin, created by students and community members in a special Freshman Seminar entitled, “The Face of Darwin: Exploring the Art/Science Borderland”. In recognition of Darwin’s 200th birthday, students from majors across campus studied Darwin’s life and the observations that led him to propose evolution by natural selection. Darwin’s face is formed by selections from his secret notebooks and the images of those organisms that influenced him most. With a beard of peppered moths, hair of barnacles and a coat of iguanas, finches, orchids and a host of other creatures, this mosaic is a profound learning experience in and of itself. The seminar was led by Diane Ullman and Donna Billick (co-directors of the Art/Science Fusion Program).

Just got back from the ASM Meeting that was in Philly last week. It was good and bad - and will write more about it soon.

But what I am writing about now relates to an annoying part of the meeting. It seems ASM has sold my name/address to various entities since I have been receiving a significant amount of junk/trash advertising things associated with microbiology. I am sure ASM gets some $$$ out of this, but at what cost to the world? The last thing I want is more trash and there seems to be no way to say no to this.

And on top of it, many science related publications also seem really keen on wrapping themselves in plastic.

In this case I am showing Nature Methods and the ASM Microbe and even the HHMI magazine wrapped in plastic. Bad Nature. Bad ASM. Bad HHMI. Sure there may be reasons for this (e.g., maybe they have an insert), but there must be non plasticy solutions. And fortunately the news from the JDRF has no plastic. Good JDRF. Here's to sciency publications getting a little greener.

Saturday, May 23, 2009

Just a quick one here. Was reading the HHMI Bulletin and saw a note about this web site they have set up on science education (see Cool Science: Home). It has all sorts of goodies for educators, kids, and others. Some of my favorite things there in looking so far include material from the Genome Consortium for Active Learning (GCAT) and the Biointeractive page. YAGTFH (Yet another good thing from HHMI).

Saturday, May 16, 2009

Just got the email below (with some key parts blotted out). It is clearly (to me) fake (although it is kind of funny in a way given the recent news about Elsevier publishing fake journals). But just in case someone else out there got the same SPAM and did not figure out it was fake, I am posting this message here.

ELSEVIER:BUILDING INSIGHTS; BREAKING BOUNDARIESMANUSCRIPTS SUBMISSION

Dear Colleague,

On behalf of all the Editors-in-chief of Elsevier Journals, we wish to Communicate to you that we are currently accepting manuscripts in all Fields of human Endeavour.All articles published will be peer-reviewed. The following types of papers are considered for publication:

Authors are invited to submit manuscripts reporting recent developments in their fields. Papers submitted will be sorted out and published in any of our numerous journals that best Fits. This is a special publication procedure which published works will be discussed at seminars (organized by Elsevier) at strategic Cities all over the world. Please maximize this opportunity to showcase your research work to the world.

The submitted papers must be written in English and describe original research not published nor currently under review by other journals. Parallel submissions will not be accepted.

Our goal is to inform authors about their paper(s) within one week of receipt. All submitted papers, if relevant to the theme and objectives of the journal, will go through an external peer-review process.

Thursday, May 14, 2009

Normally, I hate marketing slogans. But I must say I was pretty happy with the way Novozymes portrayed its "Rethink Tomorrow" branding. Yesterday, I went over to Novozymes in Davis for the opening of a new building (Novozymes has an R&D branch in Davis). It was a short and nice ceremony that included presentations by honchos from their HQ, some local Novozymes employees, as well as folks from the community including the Mayor Pro Tem of Davis Don Saylor and the head of the UC Davis Genome Center where I work, Richard Michelmore (who also happens to be the Novozymes Chair of Genomics).

What I liked about the marketing/branding discussion was how Novozymes is focused on making enzymes that can reduce the environmental impact of various industrial, agricultural, and personal processes like the making of biofuels. Sure, everyone is going green these days or attempting to in some way. But their argument that custom designed enzymes can reduce waste, allow for lower environmental impacts, etc, made sense to me. In addition, they made significant efforts to make their building a low impact building. Sure, nobody is perfect, but Novozymes seems to be making significant efforts towards the greater good even when they do not have to.

Of course, perhaps I am a little biased since I live off Novolog from NovoNordisk, a "sister" company of Novozymes (see picture at the end of my slide show on my Novolog pen ...).

Wednesday, May 13, 2009

I just got a request from a fact checker for a publication who wanted to reference my April 1 joke on Brain Doping in a story (I was not interviewed for the story). And they wanted me to sign over some rights associated with them using my name. The text of the form is below. I have been quoted and written about and even had my picture in places like the Scientific American, the New Yorker, US News and World Report, USA Today, PLoS Biology, Nature, Science, blogs, etc and not once has anyone sent me such a form. Anyone seen anything like this?

Tuesday, May 12, 2009

No plans to wear the same shirt as Marc Facciotti who is another faculty in the UC Davis Genome Center (who by the way does brilliant stuff on gene regulatory networks in yeast and halophilic archaea). But there we were in our Hamsters Love PLoS shirts. And rather than run away in shame, I begged Lizzy Wilbanks, a grad. student, to take this picture (and note the picture of Harold Varmus, Pat Brown and my brother Michael Eisen from the Genome Technology cover in the background ...)

Sunday, May 10, 2009

Looks like T. Ryan Gregory, who writes the GenoMicron blog has evolved ... he has released a new web resource on evolution - Evolver Zone. Clearly still a work in progress, it has some good collections of links to videos, journals, books and other materials about evolution. Worth checking out.

Saturday, May 09, 2009

Not much for me to add here other than to tell everyone interested in Open Science that you should look at Michael Nielsen's article: Doing science in the open - physicsworld.com. It covers a wide range of topics from secrecy to journals to the internet to online commenting to wikipedia to collaboration to FriendFeed. It has lots of interesting points in there. Hat tip toDavie Bacon / The Quantum Pontiff.

Bob Shafer, an Associate Professor at Stanford, is fighting to make information about HIV freely available. He runs a database called HIVDB that aims to make information about HIV drug resistance available to the broader community. And he has been doing this for years (note - I worked with Bob when I was a PhD student and he was getting HIVDB started - we even wrote a paper together where I helped him do some phylogenetic analysis of HIV). For that alone, Bob deserves an Open Access Pioneer award. But I am giving him one here for a fight he has taken on recently.

You see, a company called Advanced Biological Laboratories, S.A has been suing Shafer and Stanford over a patent dispute. The company seems to be trying to claim to have rights over many (or maybe they think all) uses of using computers to help doctors make medical decisions. And they have been trying to get people to license their IP/software for doing this and one way they appear to be trying to get "users" is by suing them. And Bob is one of the people they have sued.

Sadly, Stanford University appears to have given in to the lawsuits even though their validity is debatable (see The Fight of His Life which provides some of the details - Hat Tip to Bill Hooker and FriendFeed for highlighting this article) and Bob has been left hanging on his own. Instead of caving to the lawsuit and shutting down HIVDB or making it less openly available or requiring people to say they will give commercial rights to Advanced Biological Laboratories for anything they develop using the DB. And rather than cave to the lawsuits Bob is fighting back - with a website called harmfulpatents.org and with a set of letters and communications. Mind you, I know little about IP/patent laws or the legal issues behind this dispute. But if this lawsuit leads to the shutting down or restriction of HIVDB that would be proof enough to me that Advanced Biological Laboratories and the legal system that supports them is doing a disservice to the progress of science.

Friday, May 08, 2009

For those of you not in the loop on this there is a bubbling story going around the web and in some news sources about Elsevier publishing fake science/medical journals for hire. First reported by The Scientist (as far as I can tell), the story just seems to get worse and worse. Basically, it seems one branch of Elsevier published a series of journals that were little more than advertisements for Merck products while pretending to be independent journals.

The whole thing is pretty sad. The head of Elsevier as well as multiple people that have worked at Elsevier seem to have not been aware of that these were being used to pretend they were real journals. But I think one this is abundantly clear - we can cross of the list of criticisms of Open Access publishing that the costly non open access journals and publishers are protecting the world from bad science. Instead, it seems like they are in fact explicitly and purposefully pushing bad science and medicine in order to make extra money. Lovely.

The CEO of Elsevier’s Health Sciences division in the US, Michael Hansen, has now issued a statement admitting the company’s Australian office published six journals paid for by pharmaceutical companies.

Also see for example Forbes (via AP). The best source on this has been the Bloggosphere where there were a large number of discussions including

My favorite source so far has been Bill Hooker at Open Reading Frame who did some really useful digging into the details of what was being published. After his posting there has been an interesting discussion on FriendFeed (see embed below)

There also has been some other discussion on FriendFeed including the following from a Graham Steel posting:

Thursday, May 07, 2009

The Tour of California has announced it will be held May 16-23 next year (see e.g., Velonews - Amgen Tour of California May 16-23 ). Good and bad news in this. The good news is the weather will likely be a lot better than the February time slot. Bad news is this competes with the Giro and it is unclear what riders/teams will come.

The purpose of the study was to identify the effects and impacts of open access on publishing models and institutional repositories in light of national and international trends. This included the impact of open access on the quality and efficiency of scholarly outputs, specifically journal articles. The report presents options for the Research Councils to consider, such as maintaining the current variation in Research Councils’ mandates, or moving towards increased open access, eventually leading to Gold Standard.

...

In response to the study, the Chief Executives of the Research Councils have agreed that over time the UK Research Councils will support increased open access, by:

building on their mandates on grant-holders to deposit research papers in suitable repositories within an agreed time period, and;

extending their support for publishing in open access journals, including through the pay-to-publish model.

Once each year the Davis Division of the Academic Senate selects a Faculty Research Lecturer, who gives a public lecture under the auspices of the Chancellor and the Chair of the Davis Division. The lecturer is singled out for the distinction of their scholarly research, chiefly for efforts carried out while a member of the Davis faculty.

The Faculty Research Lectureship is the highest honor the Davis Division of the Academic Senate accords its members.

Please join us this evening as the campus honors our distinguished colleague

Charles “Chuck” Langley

Distinguished Professor

&

2009 Faculty Research Lecturer

Wednesday May 6, 2009

4:00 – 5:00 p.m.

A reception sponsored by Ken Burtis, Dean of the College of Biological Sciences, and

Maureen Stanton, Chair of the Department of Evolution and Ecology will follow the lecture.

Once each year the Davis Division of the Academic Senate selects a Faculty Research Lecturer, who gives a public lecture under the auspices of the Chancellor and the Chair of the Davis Division. The lecturer is singled out for the distinction of their scholarly research, chiefly for efforts carried out while a member of the Davis faculty.

The Faculty Research Lectureship is the highest honor the Davis Division of the Academic Senate accords its members.

Please join us this evening as the campus honors our distinguished colleague

Charles “Chuck” Langley

Distinguished Professor

&

2009 Faculty Research Lecturer

Wednesday May 6, 2009

4:00 – 5:00 p.m.

A reception sponsored by Ken Burtis, Dean of the College of Biological Sciences, and

Maureen Stanton, Chair of the Department of Evolution and Ecology will follow the lecture.

Tuesday, May 05, 2009

Well, this is one of those times when I feel completely blown away by some else's brilliance. And, since I am a bit on the cocky side, this does not happen all that often. But last week it did. We had a guest come and give a presentation for my lab meeting. His name is Morgan Price and he works in Adam Arkin's lab at Lawrence Berkeley Lab. He is truly pushing the bubble in terms of designing useful software for carrying out comparative and evolutionary genome analyses. Among his software/tools are FastTree andFastHMM & FastBLAST andMicrobesOnline.org

all of which are of great value in the era of ever expanding genome data accumulation. FastTree is particularly nice, allowing one to build evolutionary trees for data sets including hundreds of thousands of sequences. And on top of all of this he appears to be big on Open Access Publishing. Anyway - just a little posting here to get people to check out some of his cool computational toys.

I am looking around to find examples of undergraduate programs/majors in genomics or genome biology. I got a couple of potential examples from a post I made on friendfeed but am looking for more. What I am looking for is not just courses in genomics but majors/programs in genomics ... do they exist and if so, where and what do they look like. Any information would be helpful. Here is what I have found so far:

Biologos. All I can say is, well, I am just really baffled by the whole thing. I am all for trying to have discussions about science and religion. But I do not think the two topics are really compatible in the sense of merging them together. Science (and medicine) should be about, well, science. And religion can be about whatever it wants to be. And when we can get religious and scientific leaders together to talk about the implications of each area on the other and on the world, fine too. But merging the two together into one hybrid such as Christian Science and Creation Science? Not for me.

Thus it is with some horror that I have been browsing the web site for Francis Collins' new The BioLogos Mission | The BioLogos Foundation (f0r some other discussions of it see e.g., Larry Moran's discussion here, and PZ Myers here and Time Magazine here and US News here). BioLogos appears to be Collins attempt to promote a slight variant of "theistic evolution" which he has been discussing for years and is also in his recent book.

And whatever you may think of theistic evolution, the Biologos version of it is just icky in many ways in my mind. For example, the site has many many links and pointers to books authored by the members of the Foundation (e.g., the front page says "Among other resources, this website posts responses to many of the questions received by Collins, Giberson, and Falk since the publication of their books, including: The Language of God;Saving Darwin; and Coming to Peace With Science.") There are also other links to this page with ads for their books. Not that there is anything wrong with selling ones books, but to have a foundation whose purpose seems in a large part to promote one's books really seems distasteful.

And the details of Collins attempt to merge science and religion into a version of theistic evolution are really unclean. Basically, he is trying to argue that on the one hand science and religion are completely separate activities (I support this) but at the same time argues that God can intervene in the setting up of natural laws and in providing some guidance here and there in order to, for example, produce human beings in his image.

The web site repeats some things from Collins book that are equally illogical - such as saying that altruism can be explained by science (and even specifically saying that science is the way to explain the natural world) but then turning around and saying that science cannot explain extreme forms of altruism (and therefore implying that actually, the natural world cannot be explained by science). Which is it? Is science for the natural world or not?

What one wants to believe in terms of faith/religion is a highly personal issue. But trying to both say that science and religion are completely separate but also that they are not is just completely illogical.

Abstract

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted "worst new omics word award" to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction - ethomics will not become widely used - not soon - not ever. Thanks for pointing this one out Thomas.

Sunday, May 03, 2009

Last week I received an email also sent to a group of other local evolutionary biologists asking if one of us would be willing to participate in a "debate" with a creationist who was coming in to town to give some sort of talk. The email said, among other things:

... we have a creationist (who holds to the 6-literal day creation and young earth 6,000 year position), (name deleted), coming on our campus challenging someone to debate him.

And, well, I ignored the email as did the others apparently. Then we all got a second email a few days later:

Dear Professors,

The Creationist side is offering $300 for accepting the challenge! And another $250,000 to anyone presenting any empirical evidence for macro evolution!

Why has this offer been out there for years? Where are the experts??? Where is the evidence?? How is this possible?

If you are convinced that Darwin was right, if you accept it, if you teach it to students, as a career, then WHY DO YOU REFUSE TO DEBATE?!

You betray the students that look up to you!! Come on, Creationist don’t bite!

Sorry for this sarcastic tone, but it doesn't make sense. If you teach it in class you must be the first ones defending it.

We have a philosophy graduate wanting to debate, no science professors yet, especially Biology and Anthropology.

Please respond to this email asap!

Clearly, they people organizing this were trying to get someone to do the debate. But this strategy just convinced me that debating creationists was an absurdly silly thing. So I wrote back:

The issue is pretty simple to me. There is nothing really to debate. Creationism is not science. It is a religion driven position that pretends (and does so poorly) to be about science. I for one have perfectly pleasant interactions with many creationists and I understand their beliefs at least at some level. But just as I would not encourage physicists to debate with those who deny gravity, and just as I would not encourage chemists to debate with those who claim the periodic table is invented, I think it is inappropriate to evolutionary biologists to "debate" with creationists in this type of setting. Discussing creationism - fine. Discussing criticism of evolutionary hypotheses - fine. Having a reasonable panel discussion of science and religion - fine. Meeting with creationists to discuss their ideas about evolution - ok too. But engaging in a "debate" and thus even for a second implying that creationism stands on the same ground as evolution - completely ludicrous.

Sincerely

Jonathan Eisen

Alas, the people doing the inviting were not particularly impressed with my answer:

You Sir, are a COWARD.If it is so easy in your mind to refute Creationist's arguments, why don't you do it publically? FOR MONEY?! Your words do nothing to change the standing offer of $250,000 for evidence of Macro-Evolution. How about Actions, not Words only?

By denying there is a challenge, and at the same time refusing to accept the challenge you tell us that you're unable to defend your position.We know why you are fine with a panel discussion: because there is no Looser or Winner, you are afraid to loose, that is the real reason behind your rhetoric.

your answer is a nonanswer

Try again.

I guess they did not get my point. But anyway - I am asking readers out there - what do you think one should do? Should one debate creationists/ID supporters?

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

...

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

...

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

....

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an "Open Access Pioneer Award". Sorry I missed the talk but glad I read the article.